display.2D.histo: Display of a 2D histogram

Description

The display.2D.histo function displays the density map of a "histo2D" class object.

Usage

display.2D.histo(
  histo.2D,
  add = TRUE,
  main = NULL,
  x.lab = NULL,
  y.lab = NULL,
  x.lim = NULL,
  y.lim = NULL,
  bg = "#000000",
  i.rng = NULL,
  display.mode = c("mono.color", "rainbow.color", "line"),
  col = "#ffffff",
  alpha = 1,
  line.pc.levels = c(1, 100),
  line.lwd = 2,
  line.lty = 1
)

Value

Returns a display of the density map of histo.2D. This one must be an object of class "histo2D". See espadon.class for class definitions.

Arguments

histo.2D: "histo2D" class object.
add: Boolean indicating whether to display the background image.
main: Title of the background image. If main = NULL, the title indicates "2D histogram".
x.lab: Label of the x-axis of the background image. If x.lab = NULL, this label is histo.2D$x.file.src
y.lab: Label of the y-axis of the background image. If y.lab = NULL, this label is histo.2D$y.file.src.
x.lim: Vector, representing the range of the x-axis.
y.lim: Vector, representing the range of the y-axis.
bg: Background color of the image. By default, this color is black.
i.rng: Vector of 2 elements giving the minimum and the maximum intensity of the image. If i.rng = NULL, then the minimum is 0 and the maximum the maximum density.
display.mode: function display mode. See Details.
col: Color of the color gradient in display.mode = "mono.color", or of the level lines in display.mode = "line". By default, this color is white.
alpha: A number from 0 to 1, indicating the opacity of the image in "rainbow.color" mode. Default alpha = 1.
line.pc.levels: Vector of level lines in percent of maximum density in display.mode = "line". By default lines 1% and 100% are displayed.
line.lwd: Line thickness of the level lines in display.mode = "line".
line.lty: Type of lines for level lines in display.mode = "line".

Details

The display.mode argument can be set to three values: "mono.color", "rainbow.color", or "line". The 2D histogram graph is displayed by default in "mono.color" mode.

The "mono.color" mode displays a gradient of the color defined by the col argument, depending on the intensity of $density.map 2-dimensional array.
The "rainbow.color" mode makes a display according to the "rainbow" palette, while managing the opacity of the colors.
The "line" mode draws level lines defined in percent by the line.pc.levels argument.

Examples

Run this code

# loading of toy-patient objects (decrease dxyz for better result)
step <- 4
patient <- toy.load.patient (modality = c("ct", "mr", "rtstruct"), 
                             roi.name =  "brain", 
                             dxyz = rep (step, 3))
CT <- patient$ct[[1]]
MR <- patient$mr[[1]]
S <- patient$rtstruct[[1]]
T.MAT <- patient$T.MAT

# restriction of the volume around the RoI
CT.on.roi <- nesting.roi (CT, S, roi.name = "brain", vol.restrict = TRUE,
                          xyz.margin = c (1, 1, 1), alias = CT$description)
MR.on.CT <- vol.regrid (vol = MR, back.vol = CT.on.roi, interpolate = TRUE,
                        T.MAT = T.MAT, alias = CT$description,
                        description = NULL)
# selection of voxels included in the RoI.
roi.bin <- bin.from.roi (vol = CT.on.roi, struct = S, roi.sname = "brain",
                         verbose = FALSE)
MR.select <- vol.from.bin (MR.on.CT, roi.bin, alias = MR$description)
CT.select <- vol.from.bin (CT.on.roi, roi.bin, alias = CT$description)
# 2D histogram
H2D <- histo.2D (MR.select, CT.select, x.breaks = seq (50, 400, 10),
			  y.breaks = seq (50, 400, 10), alias = "H2D MR1 MR2")
display.2D.histo (H2D, display.mode = "mono.color", col = "#ffff00", 
                  main ="mono color mode")
display.2D.histo (H2D, display.mode = "rainbow.color", main ="rainbow mode")
display.2D.histo (H2D, display.mode = "line", main ="level lines mode",
                  line.pc.levels = c (0, 25, 50, 75, 100), col = "#ff0000")